MolNFT v1 · #112953 · protein + DNA
The crystal structure of I-dmoi E117A in complex with its target DNA and in the presence of 2MM mn
5A0W · Homing endonuclease I-dmoi: “The crystal structure of I-dmoi E117A in complex with its target DNA and in the presence of 2MM mn”. X-ray diffraction, 2 ligands (MN, CL), 10 pockets (best druggability 0.59). MolNFT v1 #112953 on…
- PDB
- 5A0W
- Type
- protein + DNA
- Length
- 701 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homing endonuclease I-dmoi; 25MER
- EC
- 3.1.-.-
- UniProt
- P21505
- Ligands
- MN, CL
- Pockets
- 10 · best druggability 0.59
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 182 | 48% helix, 25% strand | P21505 |
| B, E, H | 25MER | dna | 25 | — | — |
| C, F, I | 25MER | dna | 25 | — | — |
| D | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 191 | 52% helix, 24% strand | P21505 |
| G | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 178 | 50% helix, 26% strand | P21505 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F, G, H, I
- CL · Chloride ion · ion · 7 copies · chains A, D, E, F, G, H
- ACT · Acetate ion · additive · 5 copies · chains A, B, C, D, E, F, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.59 | 0.79 | 33 | ACT, MN |
| 2 | 262 | 0.58 | 0.79 | 36 | CL, MN, ACT |
| 3 | 243 | 0.57 | 0.79 | 36 | CL, MN, ACT |
| 4 | 274 | 0.54 | 0.76 | 28 | empty |
| 5 | 289 | 0.53 | 0.75 | 28 | empty |
Interfaces
15 interfaces between chains.
- E–F · 1302 Ų buried · 110 hydrogen bonds · nucleic-nucleic
- H–I · 1300 Ų buried · 108 hydrogen bonds · nucleic-nucleic
- B–C · 1298 Ų buried · 105 hydrogen bonds · nucleic-nucleic
- D–E · 1259 Ų buried · 30 hydrogen bonds · protein-nucleic
- G–H · 1247 Ų buried · 34 hydrogen bonds · protein-nucleic
Compared structures
- 5A0W · The crystal structure of I-dmoi E117A in complex with its target DNA and in the presence… · the same entry in another collection · chain I against I, TM-score 1.00
- P21505 · AlphaFold monomer V2.0 prediction for homing endonuclease I-dmoi (P21505) · a predicted model of the same protein · chain G against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P21505
- Elsewhere: RCSB PDB 5A0W · PDBe 5A0W · UniProt P21505
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